new tool adding

[r.papikyan]

Hi all. There is one tool for taxonomic classification that is not in galaxy. Who can help add it?

GitHub - balabanmetin/uDance

[jennaj]

Welcome, @r.papikyan

This is interesting since it is already a Snakemake workflow, so the tools would need to be wrapped (probably in a new suite of tools) then they could be used individually or as part of a Galaxy workflow.

More about Snakemake is covered in our of our tutorials here if interested → Hands-on: Make & Snakemake / Make & Snakemake / Foundations of Data Science

For the tool wrapping parts, below is how to get new development projects started:

@jennaj

Where to make the next request

1. Open an issue at the target tool’s development repository and make the request as “Wrap for Galaxy”.

or

2. Start the request at the IUC instead. GitHub - galaxyproject/tools-iuc: Tool Shed repositories maintained by the Intergalactic Utilities Commission

and

3. The third option is to wrap the tool yourself and collaborate with the two groups above.

Most of the work done for Galaxy is provided by community contributors, and the attribution procedures are very good. This includes not just the technical/coding parts, but the wrapper design (which parameters, how to model them) and scientific review (potential new tutorials, help content on the form).

If you would like to start up the discussion with the IUC to see if anyone has explored this tool already or not, or if there are any current plans I didn’t find, you can reach them at their chat. Find the link at their repository above.

You could also ask a question at the IUC’s Matrix chat. I cross-posted this over already to get it started, so feel free to join in there or they may reply here. They might also have other suggestions … but some of that might depend on where you are running Galaxy (example: your own server versus a public server). You're invited to talk on Matrix

Great, let’s start there!

[Peter_van_Heusden]

Following on from @jennaj’s comments:

1. This workflow make use of several tools that are not in the bioconda or conda-forge channels typically used by Galaxy servers, so they would need to be migrated to one of those channels to make them installable.

2. There are examples (e.g. pangolin) of tools that are interfaces to entire workflows. The decision would have to be made whether this Snakemake workflow should be “ported” to a Galaxy workflow by wrapping each tool and building a workflow or whether it should be treated as a single tool (with associated loss in flexibility and perhaps performance) and a Galaxy wrapper for the entire workflow created.

[r.papikyan]

Thank you for help and navigation.